X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=326793d054437d76271172dfd8a7646603cd1cb7;hb=d4271d32477e99e9fbbfa5db3e11f1b79324e60d;hp=b3568945760d3a17fdc86597d182d87cf98d22ea;hpb=51ff7ec3b6914f3c69b35e91e69d10c88aaf5270;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index b356894..326793d 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -274,14 +274,6 @@ public class SequenceGroup implements AnnotatedCollectionI
               endRes + 1);
       if (seqipos != null)
       {
-        seqipos.setDescription(seq.getDescription());
-        seqipos.setDBRefs(seq.getDBRefs());
-        seqipos.setSequenceFeatures(seq.getSequenceFeatures());
-        if (seq.getDatasetSequence() != null)
-        {
-          seqipos.setDatasetSequence(seq.getDatasetSequence());
-        }
-
         if (seq.getAnnotation() != null)
         {
           AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
@@ -311,6 +303,11 @@ public class SequenceGroup implements AnnotatedCollectionI
             newannot.restrict(startRes, endRes);
             newannot.setSequenceRef(seqs[ipos]);
             newannot.adjustForAlignment();
+            ContactMatrixI cm = seq.getContactMatrixFor(seq.getAnnotation()[a]);
+            if (cm!=null)
+            {
+              seqs[ipos].addContactListFor(newannot, cm);
+            }
             seqipos.addAlignmentAnnotation(newannot);
           }
         }